m3triq 0.2.4 → 0.2.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cli.js +1 -1
- package/dist/commands/md.js +4 -5
- package/package.json +1 -1
package/dist/cli.js
CHANGED
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@@ -23,7 +23,7 @@ const program = new Command();
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program
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.name('m3t')
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.description('M3TRIQ — protein-ligand analysis from the terminal')
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-
.version('0.2.
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+
.version('0.2.5')
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.option('--json', 'Output as JSON (machine-readable)')
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.hook('preAction', (thisCommand) => {
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const opts = thisCommand.optsWithGlobals();
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package/dist/commands/md.js
CHANGED
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@@ -11,8 +11,8 @@ export function registerMdCommands(program) {
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md
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.command('run')
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.option('--protein <pdb>', 'Protein PDB ID or path to .pdb file')
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-
.option('--ligand-sdf <sdf>', 'Ligand SDF content or path to .sdf file')
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-
.option('--ligand-smiles <smiles>', 'Ligand SMILES (
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+
.option('--ligand-sdf <sdf>', 'Ligand SDF content or path to .sdf file (omit for apo simulation)')
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+
.option('--ligand-smiles <smiles>', 'Ligand SMILES (omit for apo simulation)')
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.option('--diffdock-job <id>', 'DiffDock job ID (auto-fetches protein + ligand)')
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.option('--mode <mode>', 'Simulation mode: quick (10ns ~1hr) or standard (50ns ~5hrs)', 'quick')
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.option('--ns <n>', 'Override simulation duration in nanoseconds (1-100)')
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@@ -42,7 +42,7 @@ export function registerMdCommands(program) {
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else {
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params.protein_pdb = opts.protein;
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}
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-
// Resolve ligand
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+
// Resolve ligand (optional — omit for apo / protein-only MD)
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if (opts.ligandSdf) {
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if (fs.existsSync(opts.ligandSdf)) {
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params.ligand_sdf = fs.readFileSync(opts.ligandSdf, 'utf-8');
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@@ -55,8 +55,7 @@ export function registerMdCommands(program) {
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params.ligand_smiles = opts.ligandSmiles;
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}
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else {
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-
process.stderr.write('
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-
process.exit(1);
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+
process.stderr.write('Running protein-only (apo) MD — no ligand specified.\n');
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}
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}
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if (opts.ns)
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